Background: Renal oncocytoma (RO) and eosinophilic chromophobe renal cell carcinoma (ChRCC-eo) are considered to represent benign and malignant ends of the same morphological spectrum. Tumors with some, but not all, morphological features of RO or ChRCC-eo are termed "renal oncocytic tumor (ROT)” and are thought to represent an intermediate entity between RO and ChRCC-eo. However, the genetic evidence to support this assumption is scarce.Design: 13 RO, 11 ChRCC-eo and 12 ROT were subject to array-based comparative genomic hybridization. Genomic DNA was extracted from formalin-fixed, paraffin-embedded tumor and adjacent normal tissue and hybridized to Affymetrix SNP 6.0 Array chips, which contained 1.8 million genetic markers, including 906,600 single nucleotide polymorphisms (SNPs) and 946,000 probes for copy number variation (CNV) detection.Results: The total number of genes with alterations in at least 3 tumor samples of each group compared to matched adjacent normal tissue (with amplifications [+] and deletions [-] added together) was 27495, 35664 and 20535 in RO, ChRCC-eo and ROT, respectively. Table 1 listed the frequency of specific chromosomal alterations.

Chromosomal alterations

RO (n=13)

ChRCC-eo (n=11)

ROT (n=12)

-1

8 (61.5%)

10 (90.9%)

9 (75.0%)

-2

Negative

8 (72.7%)

Negative

-6

Negative

8 (72.7%)

Negative

-10

Negative

10 (90.9%)

Negative

-13

Negative

7 (63.6%)

Negative

-17

Negative

8 (72.7%)

Negative

+7

7 (53.8%)

4 (36.4%)

3 (25.0%)

+11

7 (53.8%)

Negative

3 (25.0%)

-3p21.3

(30.8%)

3 (27.3%)

7 (58.3%)

-4q12

3 (23.1%)

Negative

6 (50.0%)

Negative indicates no alteration or inconsistent results.

Deletion of chromosome 1 was seen in the majority of all 3 tumors types. -2, -6, -10, -13 and -17 were seen in the majority of ChRCC-eo, but not in RO or ROT. Amplification of chromosome 7 was seen in half of RO, a third of ChRCC-eo and a quarter of ROT. +11 were detected in half of RO, none of ChRCC-eo and a quarter of ROT. -3p21.3 and -4q12 were seen in approximately half of ROT, but in a minority or none of RO and ChRCC-eo.Conclusions: Genomic profiles suggest that ROTs are related to both RO and ChRCC-eo and have a makeup intermediated between the two. However, ROT is more closely related RO, a benign tumor, in keeping with our previous finding that all ROTs have benign clinical outcomes.Category: Genitourinary (including renal tumors)